Fei Chen (Fei Che)

Publication Activity (10 Years)

Years Active: 2019-2024
Publications (10 Years): 47

Top Topics

Diabetic Nephropathy

Plasmodium Falciparum

Single Molecule

High Throughput Sequencing

Top Venues

Nature biotechnology

Nature communications

bioRxiv : the preprint server for biology

This page only lists publications with an associated author ORCID identifier.

Publications

Gordon Fishell, Sherry Wu, Min Dai, Shang-Po Yang, Cai McCann, Yanjie Qiu, Giovanni Marrero, Jeffrey Stogsdill, Daniela Di Bella, Qing Xu, Samouil L Farhi, Evan Z Macosko, Fei Chen
Pyramidal neurons proportionately alter the identity and survival of specific cortical interneuron subtypes. Research square (2024)
Hyun Jae Lee, Marcela L Moreira, Shihan Li, Takahiro Asatsuma, Cameron G Williams, Oliver P Skinner, Saba Asad, Michael Bramhall, Zhe Jiang, Zihan Liu, Ashlyn S Kerr, Jessica A Engel, Megan S F Soon, Jasmin Straube, Irving Barrera, Evan Murray, Fei Chen, Jason Nideffer, Prasanna Jagannathan, Ashraful Haque
CD4 + T cells display a spectrum of recall dynamics during re-infection with malaria parasites. Nature communications 15 (1) (2024)
Anand G Patel, Orr Ashenberg, Natalie B Collins, Åsa Segerstolpe, Sizun J Jiang, Michal Slyper, Xin Huang, Chiara Caraccio, Hongjian Jin, Heather S Sheppard, Ke Xu, Ti-Cheng Chang, Brent A Orr, Abbas Shirinifard, Richard H Chapple, Amber Shen, Michael R Clay, Ruth G Tatevossian, Colleen Reilly, Jaimin Patel, Marybeth Lupo, Cynthia Cline, Danielle Dionne, Caroline B M Porter, Julia Waldman, Yunhao Bai, Bokai Zhu, Irving Barrera, Evan Murray, Sébastien Vigneau, Sara Napolitano, Isaac Wakiro, Jingyi Wu, Grace Grimaldi, Laura Dellostritto, Karla Helvie, Asaf Rotem, Ana Lako, Nicole Cullen, Kathleen L Pfaff, Åsa Karlström, Judit Jané-Valbuena, Ellen Z Todres, Aaron Thorner, Paul Geeleher, Scott J Rodig, Xin Zhou, Elizabeth Stewart, Bruce E Johnson, Gang Wu, Fei Chen, Jiyang Yu, Yury Goltsev, Garry P Nolan, Orit Rozenblatt-Rosen, Aviv Regev, Michael A Dyer
A spatial cell atlas of neuroblastoma reveals developmental, epigenetic and spatial axis of tumor heterogeneity. bioRxiv : the preprint server for biology (2024)
Hyun Jae Lee, Marcela L Moreira, Shihan Li, Takahiro Asatsuma, Cameron G Williams, Oliver P Skinner, Saba Asad, Michael Bramhall, Zhe Jiang, Zihan Liu, Ashlyn S Kerr, Jessica A Engel, Megan S F Soon, Jasmin Straube, Irving Barrera, Evan Murray, Fei Chen, Jason Nideffer, Prasanna Jagannathan, Ashraful Haque
CD4 + T cells display a spectrum of recall dynamics during re-infection with malaria parasites. Nature communications 15 (1) (2024)
Sherry Jingjing Wu, Min Dai, Shang-Po Yang, Cai McCann, Yanjie Qiu, Giovanni J Marrero, Jeffrey A Stogsdill, Daniela J Di Bella, Qing Xu, Samouil L Farhi, Evan Z Macosko, Fei Chen, Gordon Fishell
Pyramidal neurons proportionately alter the identity and survival of specific cortical interneuron subtypes. bioRxiv : the preprint server for biology (2024)
Xinyi Zhang, Yitong Tseo, Yunhao Bai, Fei Chen, Caroline Uhler
Prediction of protein subcellular localization in single cells. bioRxiv : the preprint server for biology (2024)
Gordon Fishell, Sherry Wu, Min Dai, Shang-Po Yang, Cai McCann, Yanjie Qiu, Giovanni Marrero, Jeffrey Stogsdill, Daniela Di Bella, Qing Xu, Samouil L Farhi, Evan Z Macosko, Fei Chen
Pyramidal neurons proportionately alter the identity and survival of specific cortical interneuron subtypes. Research square (2024)
Xinyi Zhang, Yitong Tseo, Yunhao Bai, Fei Chen, Caroline Uhler
Prediction of protein subcellular localization in single cells. bioRxiv : the preprint server for biology (2024)
Anand G Patel, Orr Ashenberg, Natalie B Collins, Åsa Segerstolpe, Sizun J Jiang, Michal Slyper, Xin Huang, Chiara Caraccio, Hongjian Jin, Heather S Sheppard, Ke Xu, Ti-Cheng Chang, Brent A Orr, Abbas Shirinifard, Richard H Chapple, Amber Shen, Michael R Clay, Ruth G Tatevossian, Colleen Reilly, Jaimin Patel, Marybeth Lupo, Cynthia Cline, Danielle Dionne, Caroline B M Porter, Julia Waldman, Yunhao Bai, Bokai Zhu, Irving Barrera, Evan Murray, Sébastien Vigneau, Sara Napolitano, Isaac Wakiro, Jingyi Wu, Grace Grimaldi, Laura Dellostritto, Karla Helvie, Asaf Rotem, Ana Lako, Nicole Cullen, Kathleen L Pfaff, Åsa Karlström, Judit Jané-Valbuena, Ellen Z Todres, Aaron Thorner, Paul Geeleher, Scott J Rodig, Xin Zhou, Elizabeth Stewart, Bruce E Johnson, Gang Wu, Fei Chen, Jiyang Yu, Yury Goltsev, Garry P Nolan, Orit Rozenblatt-Rosen, Aviv Regev, Michael A Dyer
A spatial cell atlas of neuroblastoma reveals developmental, epigenetic and spatial axis of tumor heterogeneity. bioRxiv : the preprint server for biology (2024)
Anand G Patel, Orr Ashenberg, Natalie B Collins, Åsa Segerstolpe, Sizun J Jiang, Michal Slyper, Xin Huang, Chiara Caraccio, Hongjian Jin, Heather S Sheppard, Ke Xu, Ti-Cheng Chang, Brent A Orr, Abbas Shirinifard, Richard H Chapple, Amber Shen, Michael R Clay, Ruth G Tatevossian, Colleen Reilly, Jaimin Patel, Marybeth Lupo, Cynthia Cline, Danielle Dionne, Caroline B M Porter, Julia Waldman, Yunhao Bai, Bokai Zhu, Irving Barrera, Evan Murray, Sébastien Vigneau, Sara Napolitano, Isaac Wakiro, Jingyi Wu, Grace Grimaldi, Laura Dellostritto, Karla Helvie, Asaf Rotem, Ana Lako, Nicole Cullen, Kathleen L Pfaff, Åsa Karlström, Judit Jané-Valbuena, Ellen Z Todres, Aaron Thorner, Paul Geeleher, Scott J Rodig, Xin Zhou, Elizabeth Stewart, Bruce E Johnson, Gang Wu, Fei Chen, Jiyang Yu, Yury Goltsev, Garry P Nolan, Orit Rozenblatt-Rosen, Aviv Regev, Michael A Dyer
A spatial cell atlas of neuroblastoma reveals developmental, epigenetic and spatial axis of tumor heterogeneity. bioRxiv : the preprint server for biology (2024)
Hyun Jae Lee, Marcela L Moreira, Shihan Li, Takahiro Asatsuma, Cameron G Williams, Oliver P Skinner, Saba Asad, Michael Bramhall, Zhe Jiang, Zihan Liu, Ashlyn S Kerr, Jessica A Engel, Megan S F Soon, Jasmin Straube, Irving Barrera, Evan Murray, Fei Chen, Jason Nideffer, Prasanna Jagannathan, Ashraful Haque
CD4 + T cells display a spectrum of recall dynamics during re-infection with malaria parasites. Nature communications 15 (1) (2024)
Hyun Jae Lee, Marcela L Moreira, Shihan Li, Takahiro Asatsuma, Cameron G Williams, Oliver P Skinner, Saba Asad, Michael Bramhall, Zhe Jiang, Zihan Liu, Ashlyn S Kerr, Jessica A Engel, Megan S F Soon, Jasmin Straube, Irving Barrera, Evan Murray, Fei Chen, Jason Nideffer, Prasanna Jagannathan, Ashraful Haque
CD4 + T cells display a spectrum of recall dynamics during re-infection with malaria parasites. Nature communications 15 (1) (2024)
Sherry Jingjing Wu, Min Dai, Shang-Po Yang, Cai McCann, Yanjie Qiu, Giovanni J Marrero, Jeffrey A Stogsdill, Daniela J Di Bella, Qing Xu, Samouil L Farhi, Evan Z Macosko, Fei Chen, Gordon Fishell
Pyramidal neurons proportionately alter the identity and survival of specific cortical interneuron subtypes. bioRxiv : the preprint server for biology (2024)
Sherry Jingjing Wu, Min Dai, Shang-Po Yang, Cai McCann, Yanjie Qiu, Giovanni J Marrero, Jeffrey A Stogsdill, Daniela Di Bella, Qing Xu, Samouil L Farhi, Evan Z Macosko, Fei Chen, Gordon Fishell
Pyramidal neurons proportionately alter the identity and survival of specific cortical interneuron subtypes. Research square (2024)
Andrew J C Russell, Jackson A Weir, Naeem M Nadaf, Matthew Shabet, Vipin Kumar, Sandeep Kambhampati, Ruth Raichur, Giovanni J Marrero, Sophia Liu, Karol S Balderrama, Charles R Vanderburg, Vignesh Shanmugam, Lu-Yi Tian, J Bryan Iorgulescu, Charles H Yoon, Catherine J Wu, Evan Z Macosko, Fei Chen
Publisher Correction: Slide-tags enables single-nucleus barcoding for multimodal spatial genomics. Nature (2023)
Jonah Langlieb, Nina S Sachdev, Karol S Balderrama, Naeem M Nadaf, Mukund Raj, Evan Murray, James T Webber, Charles R Vanderburg, Vahid Gazestani, Daniel Tward, Chris Mezias, Xu Li, Katelyn Flowers, Dylan M Cable, Tabitha Norton, Partha P Mitra, Fei Chen, Evan Z Macosko
The molecular cytoarchitecture of the adult mouse brain. Nature 624 (7991) (2023)
Taghreed Hirz, Shenglin Mei, Hirak Sarkar, Youmna Kfoury, Shulin Wu, Bronte M Verhoeven, Alexander O Subtelny, Dimitar V Zlatev, Matthew W Wszolek, Keyan Salari, Evan Murray, Fei Chen, Evan Z Macosko, Chin-Lee Wu, David T Scadden, Douglas M Dahl, Ninib Baryawno, Philip J Saylor, Peter V Kharchenko, David Brian Sykes
Dissecting the immune suppressive human prostate tumor microenvironment via integrated single-cell and spatial transcriptomic analyses. Nature communications 14 (1) (2023)
Andrew J C Russell, Jackson A Weir, Naeem M Nadaf, Matthew Shabet, Vipin Kumar, Sandeep Kambhampati, Ruth Raichur, Giovanni J Marrero, Sophia Liu, Karol S Balderrama, Charles R Vanderburg, Vignesh Shanmugam, Lu-Yi Tian, J Bryan Iorgulescu, Charles H Yoon, Catherine J Wu, Evan Z Macosko, Fei Chen
Slide-tags enables single-nucleus barcoding for multimodal spatial genomics. Nature (2023)
Sarah M Mangiameli, Haiqi Chen, Andrew Scott Earl, Julie A Dobkin, Daniel Lesman, Jason D Buenrostro, Fei Chen
Photoselective sequencing: microscopically guided genomic measurements with subcellular resolution. Nature methods (2023)
Blue B Lake, Rajasree Menon, Seth Winfree, Qiwen Hu, Ricardo Melo Ferreira, Kian Kalhor, Daria Barwinska, Edgar A Otto, Michael Ferkowicz, Dinh Diep, Nongluk Plongthongkum, Amanda Knoten, Sarah Urata, Laura H Mariani, Abhijit S Naik, Sean Eddy, Bo Zhang, Yan Wu, Diane Salamon, James C Williams, Xin Wang, Karol S Balderrama, Paul J Hoover, Evan Murray, Jamie L Marshall, Teia Noel, Anitha Vijayan, Austin Hartman, Fei Chen, Sushrut S Waikar, Sylvia E Rosas, Francis Perry Wilson, Susan T Crowley, Krzysztof Kiryluk, John R Sedor, Robert D Toto, Chirag R Parikh, Eric H Kim, Rahul Satija, Anna Greka, Evan Z Macosko, Peter V Kharchenko, Joseph P Gaut, Jeffrey B Hodgin, null null, Michael T Eadon, Pierre C Dagher, Tarek M El-Achkar, Kun Zhang, Matthias Kretzler, Sanjay Jain
An atlas of healthy and injured cell states and niches in the human kidney. Nature 619 (7970) (2023)
Sarah M Mangiameli, Haiqi Chen, Andrew Scott Earl, Julie A Dobkin, Daniel Lesman, Jason D Buenrostro, Fei Chen
Photoselective sequencing: microscopically guided genomic measurements with subcellular resolution. Nature methods 20 (5) (2023)
Taghreed Hirz, Shenglin Mei, Hirak Sarkar, Youmna Kfoury, Shulin Wu, Bronte M Verhoeven, Alexander O Subtelny, Dimitar V Zlatev, Matthew W Wszolek, Keyan Salari, Evan Murray, Fei Chen, Evan Z Macosko, Chin-Lee Wu, David T Scadden, Douglas M Dahl, Ninib Baryawno, Philip J Saylor, Peter V Kharchenko, David Brian Sykes
Dissecting the immune suppressive human prostate tumor microenvironment via integrated single-cell and spatial transcriptomic analyses. Nature communications 14 (1) (2023)
Caleb A Lareau, Leif S Ludwig, Christoph Muus, Satyen H Gohil, Tongtong Zhao, Zachary Chiang, Karin Pelka, Jeffrey M Verboon, Wendy Luo, Elena Christian, Daniel Rosebrock, Gad A Getz, Genevieve M Boland, Fei Chen, Jason D Buenrostro, Nir Hacohen, Catherine J Wu, Martin J Aryee, Aviv Regev, Vijay G Sankaran
Author Correction: Massively parallel single-cell mitochondrial DNA genotyping and chromatin profiling. Nature biotechnology (2023)
Abhishek Sampath Kumar, Luyi Tian, Adriano Bolondi, Amèlia Aragonés Hernández, Robert Stickels, Helene Kretzmer, Evan Murray, Lars Wittler, Maria Walther, Gabriel Barakat, Leah Haut, Yechiel Elkabetz, Evan Z Macosko, Léo Guignard, Fei Chen, Alexander Meissner
Spatiotemporal transcriptomic maps of whole mouse embryos at the onset of organogenesis. Nature genetics (2023)
Taghreed Hirz, Shenglin Mei, Hirak Sarkar, Youmna Kfoury, Shulin Wu, Bronte M Verhoeven, Alexander O Subtelny, Dimitar V Zlatev, Matthew W Wszolek, Keyan Salari, Evan Murray, Fei Chen, Evan Z Macosko, Chin-Lee Wu, David T Scadden, Douglas M Dahl, Ninib Baryawno, Philip J Saylor, Peter V Kharchenko, David Brian Sykes
Dissecting the immune suppressive human prostate tumor microenvironment via integrated single-cell and spatial transcriptomic analyses. Nature communications 14 (1) (2023)
Andrew J C Russell, Jackson A Weir, Naeem M Nadaf, Matthew Shabet, Vipin Kumar, Sandeep Kambhampati, Ruth Raichur, Giovanni J Marrero, Sophia Liu, Karol S Balderrama, Charles R Vanderburg, Vignesh Shanmugam, Lu-Yi Tian, J Bryan Iorgulescu, Charles H Yoon, Catherine J Wu, Evan Z Macosko, Fei Chen
Publisher Correction: Slide-tags enables single-nucleus barcoding for multimodal spatial genomics. Nature (2023)
Simon Mages, Noa Moriel, Inbal Avraham-Davidi, Evan Murray, Jan Watter, Fei Chen, Orit Rozenblatt-Rosen, Johanna Klughammer, Aviv Regev, Mor Nitzan
TACCO unifies annotation transfer and decomposition of cell identities for single-cell and spatial omics. Nature biotechnology (2023)
Luigi Perelli, Li Zhang, Sarah Mangiameli, Andrew J C Russell, Francesca Giannese, Fuduan Peng, Federica Carbone, Courtney Le, Hania Khan, Francesca Citron, Melinda Soeung, Truong Nguyen Anh Lam, Sebastian Lundgren, Cihui Zhu, Desiree Catania, Ningping Feng, Enrico Gurreri, Alessandro Sgambato, Giampaolo Tortora, Giulio F Draetta, Giovanni Tonon, Andrew Futreal, Virginia Giuliani, Alessandro Carugo, Andrea Viale, Timothy P Heffernan, Linghua Wang, Davide Cittaro, Fei Chen, Giannicola Genovese
Evolutionary fingerprints of EMT in pancreatic cancers. bioRxiv : the preprint server for biology (2023)
Sarah M Mangiameli, Haiqi Chen, Andrew Scott Earl, Julie A Dobkin, Daniel Lesman, Jason D Buenrostro, Fei Chen
Photoselective sequencing: microscopically guided genomic measurements with subcellular resolution. Nature methods 20 (5) (2023)
Taghreed Hirz, Shenglin Mei, Hirak Sarkar, Youmna Kfoury, Shulin Wu, Bronte M Verhoeven, Alexander O Subtelny, Dimitar V Zlatev, Matthew W Wszolek, Keyan Salari, Evan Murray, Fei Chen, Evan Z Macosko, Chin-Lee Wu, David T Scadden, Douglas M Dahl, Ninib Baryawno, Philip J Saylor, Peter V Kharchenko, David Brian Sykes
Dissecting the immune suppressive human prostate tumor microenvironment via integrated single-cell and spatial transcriptomic analyses. Nature communications 14 (1) (2023)
Sarah M Mangiameli, Haiqi Chen, Andrew Scott Earl, Julie A Dobkin, Daniel Lesman, Jason D Buenrostro, Fei Chen
Photoselective sequencing: microscopically guided genomic measurements with subcellular resolution. Nature methods 20 (5) (2023)
Kaiyi Jiang, Jeremy Koob, Xi Dawn Chen, Rohan N Krajeski, Yifan Zhang, Verena Volf, Wenyuan Zhou, Samantha R Sgrizzi, Lukas Villiger, Jonathan Samuel Gootenberg, Fei Chen, Omar O Abudayyeh
Programmable eukaryotic protein synthesis with RNA sensors by harnessing ADAR. Nature biotechnology (2022)
Paola Arlotta, Fei Chen, Simona Lodato, Troy W Margrie, Tomasz Jan Nowakowski, Thoru Pederson, Beatriz Rico
Dissecting cellular diversity of cortical GABAergic cells across multiple modalities: A turning point in neuronal taxonomy. Faculty reviews 11 (2022)
Luyi Tian, Fei Chen, Evan Z Macosko
The expanding vistas of spatial transcriptomics. Nature biotechnology (2022)
Dylan M Cable, Evan Murray, Vignesh Shanmugam, Simon Zhang, Luli S Zou, Michael Diao, Haiqi Chen, Evan Z Macosko, Rafael A Irizarry, Fei Chen
Cell type-specific inference of differential expression in spatial transcriptomics. Nature methods 19 (9) (2022)
I-Hao Wang, Evan Murray, Greg Andrews, Hao-Ching Jiang, Sung Jin Park, Elisa Donnard, Violeta Durán-Laforet, Daniel M Bear, Travis E Faust, Manuel Garber, Christina E Baer, Dorothy P Schafer, Nishigandha Phalke, Fei Chen, Evan Z Macosko, Paul L Greer
Spatial transcriptomic reconstruction of the mouse olfactory glomerular map suggests principles of odor processing. Nature neuroscience 25 (4) (2022)
Dylan M Cable, Evan Murray, Luli S Zou, Aleksandrina Goeva, Evan Z Macosko, Fei Chen, Rafael A Irizarry
Robust decomposition of cell type mixtures in spatial transcriptomics. Nature biotechnology (2021)
Tongtong Zhao, Zachary D Chiang, Julia W Morriss, Lindsay M LaFave, Evan M Murray, Isabella Del Priore, Kevin Meli, Caleb A Lareau, Naeem M Nadaf, Jilong Li, Andrew Scott Earl, Evan Z Macosko, Tyler Jacks, Jason D Buenrostro, Fei Chen
Spatial genomics enables multi-modal study of clonal heterogeneity in tissues. Nature 601 (7891) (2021)
Brian Cleary, Brooke Simonton, Jon Bezney, Evan Murray, Shahul Alam, Anubhav Sinha, Ehsan Habibi, Jamie L Marshall, Eric S Lander, Fei Chen, Aviv Regev
Compressed sensing for highly efficient imaging transcriptomics. Nature biotechnology 39 (8) (2021)
Hattie Chung, Christopher N Parkhurst, Emma M Magee, Devan Phillips, Ehsan Habibi, Fei Chen, Bertrand Z Yeung, Julia Waldman, David Artis, Aviv Regev
Joint single-cell measurements of nuclear proteins and RNA in vivo. Nature methods 18 (10) (2021)
Samuel G Rodriques, Linlin M Chen, Sophia Liu, Ellen D Zhong, Joseph R Scherrer, Edward S Boyden, Fei Chen
RNA timestamps identify the age of single molecules in RNA sequencing. Nature biotechnology 39 (3) (2020)
Andrew C Payne, Zachary D Chiang, Paul L Reginato, Sarah M Mangiameli, Evan M Murray, Chun-Chen Yao, Styliani Markoulaki, Andrew Scott Earl, Ajay S Labade, Rudolf Jaenisch, George M Church, Edward S Boyden, Jason D Buenrostro, Fei Chen
In situ genome sequencing resolves DNA sequence and structure in intact biological samples. Science (New York, N.Y.) 371 (6532) (2020)
Jamie L Marshall, Benjamin R Doughty, Vidya Subramanian, Philine Guckelberger, Qingbo Wang, Linlin M Chen, Samuel G Rodriques, Kaite Zhang, Charles P Fulco, Joseph Nasser, Elizabeth J Grinkevich, Teia Noel, Sarah Mangiameli, Drew T Bergman, Anna Greka, Eric S Lander, Fei Chen, Jesse M Engreitz
HyPR-seq: Single-cell quantification of chosen RNAs via hybridization and sequencing of DNA probes. Proceedings of the National Academy of Sciences of the United States of America 117 (52) (2020)
Robert R Stickels, Evan Murray, Pawan Kumar, Jilong Li, Jamie L Marshall, Daniela Di Bella, Paola Arlotta, Evan Z Macosko, Fei Chen
Highly sensitive spatial transcriptomics at near-cellular resolution with Slide-seqV2. Nature biotechnology 39 (3) (2020)
Caleb A Lareau, Leif S Ludwig, Christoph Muus, Satyen H Gohil, Tongtong Zhao, Zachary Chiang, Karin Pelka, Jeffrey M Verboon, Wendy Luo, Elena Christian, Daniel Rosebrock, Gad A Getz, Genevieve M Boland, Fei Chen, Jason D Buenrostro, Nir Hacohen, Catherine J Wu, Martin J Aryee, Aviv Regev, Vijay G Sankaran
Massively parallel single-cell mitochondrial DNA genotyping and chromatin profiling. Nature biotechnology 39 (4) (2020)
Haiqi Chen, Sophia Liu, Samuel Padula, Daniel Lesman, Kettner Griswold, Allen Z Lin, Tongtong Zhao, Jamie L Marshall, Fei Chen
Efficient, continuous mutagenesis in human cells using a pseudo-random DNA editor. Nature biotechnology 38 (2) (2019)
Samuel G Rodriques, Robert R Stickels, Aleksandrina Goeva, Caroline A Martin, Evan Murray, Charles R Vanderburg, Joshua Welch, Linlin M Chen, Fei Chen, Evan Z Macosko
Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science (New York, N.Y.) 363 (6434) (2019)